[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

[Justin Lemkul]

On 9/30/14 7:06 AM, Anurag Dobhal wrote:
> Thank you Justin for your reply
>
> as per your suggestion i verified the contents in confout.gro but i was
> unable to check file as when i am clicking on it to open it I am getting an
> message that file is of unknown type.
>

A .gro file is not simply something that you click on to magically open.  It's 
just a listing of coordinates.  Visualize it in VMD.  Inspect its contents with 
a text editor.

-Justin

> I again repeated the tutorial and I am getting the same things.
>
> Thank you again for your time.
>
> On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/30/14 5:51 AM, Anurag Dobhal wrote:
>>
>>> Hello gromacs users.
>>>
>>>
>>> I am running GROMACS Tutorial of  KALP15 in DPPC.
>>>
>>> I am in the step define box and solvate.
>>>
>>> after the command
>>>
>>> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
>>> area_shrink1.dat
>>>
>>>
>>> i am getting an error as
>>>
>>> Use of uninitialized value $box_x in multiplication (*) at
>>> inflategro.pl line 339.
>>> Use of uninitialized value $box_y in multiplication (*) at
>>> inflategro.pl line 340.
>>> Scaling lipids....
>>> There are 0 lipids...
>>> Illegal division by zero at inflategro.pl line 380.
>>>
>>> I am repeating the step third time and I am getting the same error.
>>>
>>> please help me how to skip this error.
>>>
>>>
>> I suggested you verify the contents of confout.gro are sensible.  What did
>> you learn?
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================